Biotech Executive Offers Glimpse of Testing Future

Ariela Katz

Published: Saturday, May 27, 2017

Vince Miller, MD

In December, Foundation Medicine, a leader in the field of molecular testing, strengthened its industry position by gaining its first FDA approval for a companion diagnostics test: Foundation Focus CDx BRCA, which can detect both germline and somatic BRCA1/2 mutations in women with ovarian cancer who are candidates for the PARP inhibitor rucaparib (Rubraca). The test also is the first next-generation sequencing-based companion diagnostic that the agency has approved.

The 8-year-old company, which has attracted significant academic interest, including a partnership with Memorial Sloan Kettering Cancer Center, this year not only began seeing revenue from the Foundation Focus CDx BRCA but also for the first time reached a major milestone when Medicare began paying for its FoundationOne large panel genomic assay, specifically in cases of patients with non–small cell lung cancer. The Cambridge, Massachusetts-based company also has reported further clinical use of its FoundationOne Heme hematological biomarker test and its FoundationACT blood-based circulating tumor DNA assay.

With these achievements under its belt, Foundation Medicine’s chief medical officer, Vince Miller, MD, spoke with OncologyLive® about the company’s testing ambitions, the potential for commercial payers to initiate coverage of its tests, and the company’s increasing roster of business partners in the pharmaceutical industry.

Miller said Foundation Medicine is now anticipating FDA approval of the large-panel FoundationOne assay as a universal companion diagnostic, which he said would be key to the company’s fortunes. Using next-generation sequencing, the assay can test for more than 300 cancer-related genes. However, Miller said various other barriers exist. Genetic testing needs to become a routine part of the therapeutic process, and doctors need help in interpreting the actionable results of these complex tests, he said.

What sets the large-panel test FoundationOne apart from other genomic assays?

We know there’s an increasing number of targeted therapies, and that even though a certain percentage will not be approved by the FDA, the trend is that as each month goes by, more and more targeted therapies are available to patients. A growing number of these treatments are also associated with companion diagnostics tests.

There has been an increase in demand to find biomarkers relative to disease states that could be tied to FDA-approved therapies and potentially accelerate the development of future targeted therapies. In cancer, many biopsy tests take very small samples, and so if one relies on multiple gene assays, not only do costs rise, but also the chance of getting all the needed results drops.

it’s comprehensive: across 320-plus genes; we assess them all simultaneously in the same assay for every patient for all the main classes of DNA alterations, including all the amplifications of genes, such as the HER2 gene in breast cancer; deletions in certain genes, such as the exon gene in lung cancer; point mutations, such as the BRAF mutation in melanoma; and the fusion genes, such as ALK in lung cancer.

Normally, to assay for these markers, you would need to cobble together different technologies with various sensitivities and specificities, often with unpublished false-negative and false-positive rates that you don’t know. This leads to the problem of insufficient tissue sample and a lack of clarity or confidence in the results. What FoundationOne does is take a single piece of tissue and, under what will be a regulated environment after we’ve published and demonstrated a precedent in clinical validation, it evaluates all these genes simultaneously.

Not only are we synching up patients with FDA-approved drugs for given indications, but also we can match patients from a DNA standpoint with many different targeted therapy clinical trials. There are more than 1000 targeted therapeutics across over 100 genes of interest under study presently, and several thousand trials involving those targeted therapeutics. So, this is a great tool to allow a doctor treating patients with cancer to see if their patient is eligible for an FDA-approved therapy or to evaluate, from a molecular standpoint, whether they’re eligible to participate in specific clinical trials.

We recently had our first FDA approval of a companion diagnostic that was developed as the assay for Clovis Oncology’s drug rucaparib and that’s FoundationFocus CDx BRCA. It detects both germline and somatic BRCA1/2 mutations in women with ovarian cancer to predict increased sensitivity to that drug.